From 1edfe481940024fa5d48198204267740397a87ae Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 15 Apr 2009 19:09:18 +0000
Subject: [PATCH] Better debugging output with .debug

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@433 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../org/broadinstitute/sting/gatk/traversals/TraverseByLoci.java | 1 +
 1 file changed, 1 insertion(+)

diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLoci.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLoci.java
index 2a31b8538..416521a21 100644
--- a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLoci.java
+++ b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLoci.java
@@ -111,6 +111,7 @@ public class TraverseByLoci extends TraversalEngine {
 
             // actually get the read and hand it to the walker
             LocusContext locus = iter.next();
+            logger.debug(String.format("Crossing locus %s with %d reads", locus.getLocation(), locus.numReads()));
             if ( DOWNSAMPLE_BY_COVERAGE )
                 locus.downsampleToCoverage(downsamplingCoverage);